101 questions with a bioinformatician #12: Karen Eilbeck

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This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting theirbioinformatics careers.

Karen Eilbeck is an Associate Professor of Biomedical Informatics at the University of Utah. Karen comes from a long line of distinguished bioinformaticians who learned their skills at the highly regarded Bioinformatics M.Sc. program at the UK's University of Manchester (although they do let some riff-raff in).

If you read Karen's research statement, you will see that there is a clear focus to her work:

Quality control of genomic annotations; Management and analysis of personal genomics data; Ontology development to structure biological, genomic and phenotypic data

In helping build both the Gene Ontology and Sequence Ontology resources, Karen's work has led to the development of powerful structured vocabularies that help ensure that all biologists can speak the same language. Developing ontologies is harder than you might imagine, especially when you are trying to generate precise definitions for very nebulous concepts such as what is a gene?

You can find out more about Karen from the Eilbeck Lab website. And now, on to the 101 questions...



001. What's something that you enjoy about current bioinformatics research?

I think genomic analysis is fascinating. The human genetics stories suck me in, where bioinformatics is used to find the variant causing the phenotype. The story does not end there, tests are developed, or therapies targeted. 


010. What's something that you *don't* enjoy about current  bioinformatics research?

This is a positive and a negative. I like being part of collaborative projects. It is exciting and things get done. The downside is the amount of time on the phone. It is not something I would ever have anticipated. Conference calls either go OK, or someone is heavy breathing in a train station and hasn’t put their phone on mute. The video conference is either delayed or the resolution is not great. One of my colleagues shared this video with me, which has a lot of truth to it.


011. If you could go back in time and visit yourself as an 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

Only a single piece? OK, take your math classes more seriously. I wish I had known how to program when I was doing statistics classes. Instead of using packages like SPSS it may have been more educational to implement tests myself. 


100. What's your all-time favorite piece of bioinformatics software, and why?

I am totally in love with a piece of software right now called Phevor, which re-ranks variant prioritization based on phenotype descriptions and uses a variety of ontologies to do its magic. Which brings me to my all time fave tool: OBO-Edit. I think that OBO-edit was underrated. This tool was developed by the Gene Ontology consortium to build their ontology, and it rapidly became adopted by the biological community. It is easy to use and underpinned many of the ontologies in the bioinformatics domain today. The lead developer for a long time was John Richter who is also a stand-up comedian that went on to work for Google. OBO-edit will always have a place in my heart


101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality?

W (A or T). On the one hand it's reserved and to the point (A), on the other hand it's full of energy and works well with others (T). Also, much like my name, there is confusion when it comes to pronunciation (Eel-beck or I’ll-Beck).

W and its skinny friend V, seem interchangeable regarding pronunciation. A friend of mine calls a character from Star Wars Darth Wader, which make me smile.